MBG 2040 Final Review PDF

DNA replication (lectures 2-3) Theta replication:circular dna (like in bacteria copies itself), dna opens at origin, bubble forms as dna strands are split apart, two enzymes work in opposite directions to copy DNA, two new DNA circles separate and now there are 2 copies. Rolling circle replication:...

DNA replication (lectures 2-3) Theta replication:circular dna (like in bacteria copies itself), dna opens at origin, bubble forms as dna strands are split apart, two enzymes work in opposite directions to copy DNA, two new DNA circles separate and now there are 2 copies. Rolling circle replication: Nick is made in 1 strand of dna, intact strand act as template while nicked strand rolls out and gets copied. End= makes a long continuous strand that can later be cut into smaller pieces, common in viruses and plasmids. dNTPs: building block of DNA, has 1 deoxyribose sugar, nitrogenous base, 3 phosphate groups. RNA primer: short strand of RNA that helps start DNA replication. Initiator Protein: starts process of DNA replication, main role is to recognize and bind to origin of replication Helicase: unwinds the DNA double helix Gyrase: introduces negative supercoils and prevents dna breakage, prevent fron getting tangled or breaking as it is unwound. SSBP: protein that binds to single strand DNA to keep it stable and prevent it forming unwanted structures. During dna replication/ repair, dna becomes single strand and ssbp attach themselves and protects them from breaking or rejoining w other strands to make sure dna can be fixed or copied correctly. Primase: enzyme that creates short piece of RNA called primer during DNA replication. DNA POL 1: remove RNA primer and replace w DNA nucleotides. DNA POL 2: Involved in DNA repair and helps fix errors during replication. DNA POL 3: Main enzyme for DNA replication, adds nucleotides to growing DNA strand/ Ligase: helps glue together DNA strands DNA Pol alpha: start DNA replication by adding initial RNA-DNA primer to dna strand. DNA Pol epsilon:synthesizing leading strand during replication. DNA Pol delta: synthesizes the lagging strand during DNA replication and helps w repair. Nucleosome: basic unit of DNA packaging in cells. Consists of a segment of DNA wrapped around a core of proteins called histones. Histone: proteins that help organize and pack DNA into a compact structure called a nucleosome. Chromatin: material that makes up chromosomes, consists of dna wrapped around histone proteins, forming nucleosomes. Telomere: protective cap at the end of each chromosome. Protects from degradation and sticking to other chromosomes. Telomerase: enzyme that adds repetitive DNA sequences to end of telomeres, maintaining their length. MCM Complex: proteins that unwind DNA so it can be copied during replication, acts as motor that helps open up the DNA for other enzymes to work. ORC: group of proteins that bind to the origin of replication on DNA, acts as a starter by marking the spot where DNA replication will begin, helps recruit other proteins to start unwinding copying DNA. Transcription & RNA processing (lectures 4-5) rNTPs: building blocks of RNA, consists of nitrogenous base, ribose sugar and three phosphate groups linked in a chain RNA Pol Holoenzyme-5 components: alpha subunits (2copies) important for enzyme assembly and interaction w regulatory proteins. Beta subunit catalyzes RNA synthesis. Beta prime binds DNA and ensures stability. Omega stabilizes the core enzyme structure. Sigma factor guides the holoenzyme to specific promoter regions on DNA to initiate transcription. Rho dependent vs Rho independent: rho depends on Rhp protein which binds to a specific RNA sequence, moves along the RNA and disrupts the RNA-DNA hybrid at the transcription bubble to terminate transcription. Rho independent relies on hairpin followed by a bunch of U’s to destabilize the RNA-DNA hybrid causing RNA polymerase to release the RNA w/o need for Rho. Kozak Sequence: specific sequence that initiates translation 5’GCCa or gCCAUGG3’ EF-G: facilitates translocation EF-Tu: delivers aminoacyl-tRNA. Ef-Ts: acts as a guanine nucleotide exchange factor. RF-1: recognizes UAG and UAA stop codons and promotes the release of the completed polypeptide from ribosome. RF-2: recognizes the UGA and UAA stop codons, facilitating the polypeptide release. RF-3: GTPase helps to recycle RF-1, RF-2 by releasing them from ribosome after they complete their function. Uses GTP hydrolysis for this process. All of these release factors work together to ensure translation stops accurately at the correct stop codon. RNA POL 1: transcribes rRNA genes, for ribosome assembly. RNA POL 2: transcribes mRNA, snRNA, and miRNA, making it critical for producing more protein coding RNA. RNA POL 3: transcribes tRNA, 5S rRNA and other small rnas RNA POL 4: synthesizes siRNAs that guide the silencing machinery to specific DNA regions. RNA POL 5: makes scaffold RNAs to guide gene silencing machinery. TFIIA: stabilizes the binding of TFIID to the promoter. TFIIB: helps RNA Polymerase II recognize the start site and bind to TFIID. TFIID: contains the TBP or the TATA-binding protein and helps RNA POL II bind to the promoter. TFIIE: recruits the regulates TFIIH TFIIF: escorts RNA Pol II to promoter and stabilizes the complex TFIIH: unwinds DNA, phosphorylates RNA Pol II to start transcription. RAT1: a 5’ to 3’ exonuclease in eukaryotes thatplay a key role in transcription termination, by degrading RNA from 5’ end when transcription doesn’t stop properly. PIC: all the TFII’s assemble the PIC.group of proteins that assemble at the promoter and help RNA Pol II start transcription, prepares the DNA and RNA Pol to begin making RNA. Mediator: protein complex that links transcription factors to RNA Pol II, regulates gene expression by facilitating communication between enhancers, promoters and the transcription machinery. RNA processing (lectures 4-6) Co-linearity: the direct correspondence between the sequence of nucleotides in DNA and sequence of amino acids in protein. So in simple terms, the order of bases in gene matches the order of codons in mRNA and then translates into amino acid sequence of the protein. 5’ UTR: section of mRNA that is located before the start codon, plays role in regulating translation and how the mRNA is processed and stability. Protein coding region: part of mRNA that contains the codons which are translated into a protein. Starts w start codon (AUG) and ends w a stop codon. 3’ UTR: part of mRNA after stop codon.doesn’t code for protein but helps regulate mRNA stability, translation efficiency, and gene expression. snRNAs: type of RNA that helps w splicing in nucleus, process of removing introns from pre-mRNA to create mature mRNA. Spliceosome: complex of snRNAs and proteins that removes introns from pre-mRNA and joins exons together to create mature mRNA. 3’ Poly A Tail: string of adenine nucleotides added to end of mRNA, protects mRNA from degradation, helps mRNA exit nucleus, assisting in translation by helping the ribosome recognize the mRNA. 5’ cap: modified guanine added to beginning of mRNA, functions include protecting mRNA from degradation, helping mRNA leave nucleus, and assisting the ribosome in recognizing and starting translation. Intron Branch point: special adenine in middle of an intron, helps in splicing process by forming a loop called a lariat that helps remove the intron and connect the exons together to make the final mRNA. 5’ splice site: beginning of an intron where splicing starts. 3’ splice site: end of an intron where splicing ends. Lariat: loop like structure formed during RNA splicing when the intron is cut out. Lecture 7 RNA molecules & RNA processing Alternative splicing: where different combos of exons are joined together to create multiple RNA versions from the same gene, leading to different proteins. Multiple cleavage sites: spots in RNA where it can be cut in different places leading to RNA versions. Allowing more variety in RNA molecules and contributing to alternative splicing. Guide RNAs: RNA molecules that help other molecules like endonucleases find specific places in genome, directing the enzymes to correct DNA or RNA target for processes like RNA editing or CRISPR gene editing Apoplipoprotein -B: protein that plays key role in transporting lipids in blood, major component of lipoproteins, help w lipid metabolism and important for proper lipid distribution in body. tRNA: molecules that bring amino acids to ribosome during protein synthesis. Each tRNA has anitcodon that matches a specific mRNA codon ensuring the correct amino acid is added to growing protein chain. rRNA: help make up ribosome, help read mRNA and guide process of linking amino acids tg. Ribosome: synthesizes proteins by reading mRNA and linking aa together in correct order, play big role in translation during protein production. snRNAs: involved in splicing, removes introns from pre-mRNA and joins exons together to make mature mRNA, key components of splicesome. snoRNAs: modify rRNA by adding methyl groups to specific nucleotides which are important for the proper functioning of ribosomes. siRNA: involved w gene silencing.bind to mRNA and promote their degradation, preventing production of specific proteins, this process is part of the RNA interference pathway. miRNA: regulates gene expression by binding to mRNA and blocking its translation or causing its degradation preventing certain proteins from being made. Crispr RNA: help identify and cut the target DNA, allowing for gene editing by removing or altering parts of the DNA. LncRNA: type of rna that doesn’t code for proteins but play a role in regulating gene expression, chromatin structure and other cellular processes, helps control how genes are turned on or off. Lecture 8 Genetic Code and Translation One gene-one colinear polypeptide: each gene directly codes for a specific protein w a sequence that matches the sequence of the gene’s nucleotides. The order of nucleotides in the gene determines the order of amino acids in the protein. 4 levels of organization of proteins: primary, secondary, tertiary, quaternary. (think biochem) Wobble Hypothesis: explains how a single tRNA can recognize multiple codons that code for the same amino acid. Suggests that the third position of the codon can pair less strictly w the tRNA, allowing flexibility in codon-anticodon matching. Lecture 9- Genetic Code and Translation Aminoacyl tRNA synthetase: enzyme that attaches the correct amino acid to its matching tRNA. Process is important cuz ensures the right amino acid is added to the growing protein chain during translation. AMP: molecule that helps w energy and cell signalling, made when ATP loses two of its phosphate groups and helps regulate the cell’s energy use. 16S rRNA: part of the small subunit of the ribosome in bacteria. Helps the ribosome bind to the mRNA and ensures correct codons are matched w the right tRNA during protein synthesis. 30S small ribosomal subunit: in bacteria that helps read the mRNA and ensures the correct tRNA matches w the mRNA codons during protein synthesis. Helps hold the mRNA and tRNA in place for proper translation. Shine-Dalgarno sequence: short, specific RNA sequence in bacteria that helps ribosome recognize the start site of translation, located just right before the start codon on the mRNA and pairs with the 16S rRNA of the small ribosomal subunit to position the ribosome correctly for protein synthesis. IF-1: bind to ribosome’s A site, preventing premature tRNA binding and ensuring the correct start. IF-2: helps bring the initiator tRNA to ribosome and uses GTP for energy. IF-3: binds to the ribosome’s small subunit, ensuring it doesn’t prematurely bind to the large subunit and helping the ribosome recognize the mRNA. All three tg ensures proper assembly of the ribosome and the tRNA at the start codon for translation to begin. Fmet tRNA: special tRNA that carries the amino acid formylmethionine, which is used as the first amino acid in protein synthesis in bacteria, helps initiate translation by binding to start codon on the mRNA, allowing the ribosome to begin protein production. EPA sites: 3 binding sites on the ribosome during protein synthesis, E site where the empty tRNA exits the ribosome after amino acid is added. P site which holds the tRNA with the growing polypeptide chain. A site where the new tRNA carrying the next amino acid enters the ribosome. These sites work together to add amino acids to growing protein. MET tRNA: carries amino acid methionine and is used to initiate protein synthesis in eukaryotes. Binds to the start codon on the mRNA, setting the stage for the ribosome to begin translating the mRNA into a protein. Gene mutations and DNA repair (lectures 10-13) Somatic Mutations: occur only in body cells and affect only that individual and not offspring. Germinal Mutations: occur in egg or sperm and can be passed down to future generations. :( Base Substitutions (Transition, Transversion): transition- a purine replaces another purine or a pyrimidine replacing another pyrimidine. Transversion- a purine replaces a pyrimidine or vice versa. Insertions: adding extra nucleotides into the DNA sequence. Deletions:removing nucleotides from the DNA sequence. Frameshift mutations: mutations that shift the reading frame of the gene due to insertions and deletions, changing the entire protein. In-frame mutations and deletions: mutations or deletions that don’t shift the reading frame but still alter the protein. Tautomeric shifts: changes in the chemical structure of bases that lead to incorrect base pairing. Dynamic mutation: mutations that change in severity over generations, often involving repeat expansions. Forward mutation: mutation that changes a gene’s function in a typical direction. Reverse Mutation: mutation that restores the original gene’s function. Missense Mutation: mutation that changes one amino acid in a protein, possibly altering its function. Nonsense Mutation: mutation that turns an amino acid codon into a stop codon, shortening the protein. Silent mutation: mutation that changes the codon but does not change the amino acid or protein function. Neutral mutation: mutation that doesn’t affect the protein’s function, often due to silent mutations. Loss of function mutation: mutation that reduces or eliminates the protein’s function. Gain of function mutation: mutation that results in a protein with a new or enhanced function. Conditional mutation: mutation that causes a phenotype only under certain conditions (temp) Lethal Mutation: mutation that causes death often in early development. Suppressor Mutation: mutation that compensates for or reverses the effects of another mutation, restoring normal function. Lecture 12 Gene mutations and DNA repair Spontaneous Replication Errors: mistakes made during DNA copying that happen naturally without external causes. Tautomeric Shifts: a rare change in the structure of DNA bases, causing them to pair incorrectly during replication. Mispairing due to other structures: when unusual shapes in DNA cause the wrong bases to pair up. Incorporated errors and replicated errors: incorporated- when the wrong base is added to the DNA during copying. Replicated- when an incorporated error is copied into the new DNA strand making it permanent. Deletions & Insertions: deletion is when a piece of DNA is missing. Insertion is extra dna added. Spontaneous chemical changes: Natural changes in DNA bases that alter their structure or pairing. Depurination: the loss of a purine base (adenine or guanine) from DNA Deamination: removal of an amino group from a dna base, changing it to a different molecule. Methylated cytosine: a cytosine base w a chemical (methyl) group added, which makes it prone to mutation. Chemically induced mutations: DNA changes caused by exposure to harmful chemicals. Base analogs (know the examples) : molecules that mimic DNA bases and get inserted during replication, causing mutations. Deaminating chemicals (know the example) : chemicals that remove amino groups from DNA bases, altering their structure. Hydroxylamine: chemical that changes cytosine so it paired incorrectly with adenine. Oxidative Radicals: Highly reactive molecules that damage DNA by altering its structure. Intercalating Agents: Chemicals that slide between DNA bases, causing insertions or deletions during replication. Radiation: energy like x rays or UV light that damages DNA by breaking it or creating abnormal bonds. Lecture 13 Gene mutations and DNA repair Repair of single stranded sequences: fixes damage in one strand of DNA using the undamaged strand as a template. Mismatch repair: fixes errors where the wrong bases are paired after DNA replication. Direct repair or reversal of DNA damage: fixes damaged DNA without cutting it, by directly reversing the damage. Base-Excision Repair: removes and replaces a damaged base in DNA by cutting it out and filling in the correct base. Nucleotide-Excision Repair: removes a chunk of damaged DNA(few bases) and replaces it with the correct sequence. Repair of double stranded breaks: fixes breaks where both strands of DNA are cut. Homology Directed Repair: uses a matching DNA sequence as a guide to repair the double stranded breaks accurately. Nonhomologous End Joining: fixes double stranded breaks by directly joining the broken ends, which can sometimes cause errors. Photolyase: an enzyme that uses light energy to fix DNA damage caused by UV rays. DNA Glycosylases: enzymes that remove damaged or incorrect DNA bases as part of the base-excision repair. Endonuclease: enzyme that cuts DNA within a strand to remove damaged sections. Lecture 14 Transposable Genetic Elements Jumping Genes: pieces of DNA that can move to different parts of the genome. Transposable element: another name for jumping genes, these are DNA segments that cna move within the genome. Flanking direct repeats: short, identical sequences found on both sides of a transposable element after it inserts into the DNA. Transposase enzyme: protein that helps a transposable element cut itself out of DNA and moves it to a new location. Terminal inverted repeats: DNA sequences at the ends of a transposable element that are mirror images of each other and help it move. Class I Retrotransposons (RNA intermediate): jumping genes that copy themselves through an RNA step before inserting into DNA. Class II Retrotransposons (DNA transposons- catalyzed by transposase) : jumping genes that move directly as DNA, using the transposase enzyme. piRNAs: small RNAs that protect DNA from jumping genes by silencing them. Mutagenic effect: the ability to cause mutations, like when jumping genes disrupt normal DNA.